<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.16"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>ClaraGenomicsAnalysis: claragenomics::cudamapper::Index Class Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
 <tbody>
 <tr style="height: 56px;">
  <td id="projectalign" style="padding-left: 0.5em;">
   <div id="projectname">ClaraGenomicsAnalysis
   &#160;<span id="projectnumber">0.4.0</span>
   </div>
  </td>
 </tr>
 </tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.16 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
var searchBox = new SearchBox("searchBox", "search",false,'Search');
/* @license-end */
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
$(function() {
  initMenu('',true,false,'search.php','Search');
  $(document).ready(function() { init_search(); });
});
/* @license-end */</script>
<div id="main-nav"></div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
     onmouseover="return searchBox.OnSearchSelectShow()"
     onmouseout="return searchBox.OnSearchSelectHide()"
     onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0" 
        name="MSearchResults" id="MSearchResults">
</iframe>
</div>

<div id="nav-path" class="navpath">
  <ul>
<li class="navelem"><b>claragenomics</b></li><li class="navelem"><b>cudamapper</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a></li>  </ul>
</div>
</div><!-- top -->
<div class="header">
  <div class="summary">
<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="#pub-static-methods">Static Public Member Functions</a> &#124;
<a href="classclaragenomics_1_1cudamapper_1_1Index-members.html">List of all members</a>  </div>
  <div class="headertitle">
<div class="title">claragenomics::cudamapper::Index Class Reference<span class="mlabels"><span class="mlabel">abstract</span></span><div class="ingroups"><a class="el" href="group__cudamapper.html">CUDA mapper package</a></div></div>  </div>
</div><!--header-->
<div class="contents">

<p><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a> - manages mapping of (k,w)-kmer-representation and all its occurences.  
 <a href="classclaragenomics_1_1cudamapper_1_1Index.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="index_8hpp_source.html">index.hpp</a>&gt;</code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:afcaccc9f9526d9c66280eca17ff3a4ac"><td class="memItemLeft" align="right" valign="top"><a id="afcaccc9f9526d9c66280eca17ff3a4ac"></a>
virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#afcaccc9f9526d9c66280eca17ff3a4ac">~Index</a> ()=default</td></tr>
<tr class="memdesc:afcaccc9f9526d9c66280eca17ff3a4ac"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor. <br /></td></tr>
<tr class="separator:afcaccc9f9526d9c66280eca17ff3a4ac"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a876d5e82f9fc36f481854f7d84e5fc80"><td class="memItemLeft" align="right" valign="top">virtual const thrust::device_vector&lt; representation_t &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a876d5e82f9fc36f481854f7d84e5fc80">representations</a> () const =0</td></tr>
<tr class="memdesc:a876d5e82f9fc36f481854f7d84e5fc80"><td class="mdescLeft">&#160;</td><td class="mdescRight">returns an array of representations of sketch elements  <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a876d5e82f9fc36f481854f7d84e5fc80">More...</a><br /></td></tr>
<tr class="separator:a876d5e82f9fc36f481854f7d84e5fc80"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5cfe03b47850170ec64d61d2dbef0401"><td class="memItemLeft" align="right" valign="top">virtual const thrust::device_vector&lt; read_id_t &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5cfe03b47850170ec64d61d2dbef0401">read_ids</a> () const =0</td></tr>
<tr class="memdesc:a5cfe03b47850170ec64d61d2dbef0401"><td class="mdescLeft">&#160;</td><td class="mdescRight">returns an array of reads ids for sketch elements  <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a5cfe03b47850170ec64d61d2dbef0401">More...</a><br /></td></tr>
<tr class="separator:a5cfe03b47850170ec64d61d2dbef0401"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a66e5d024befc410221610f454eff7183"><td class="memItemLeft" align="right" valign="top">virtual const thrust::device_vector&lt; position_in_read_t &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a66e5d024befc410221610f454eff7183">positions_in_reads</a> () const =0</td></tr>
<tr class="memdesc:a66e5d024befc410221610f454eff7183"><td class="mdescLeft">&#160;</td><td class="mdescRight">returns an array of starting positions of sketch elements in their reads  <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a66e5d024befc410221610f454eff7183">More...</a><br /></td></tr>
<tr class="separator:a66e5d024befc410221610f454eff7183"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5824f352fd89f69c9acc14430a3aa6cd"><td class="memItemLeft" align="right" valign="top">virtual const thrust::device_vector&lt; <a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a83beb5c091c4b0bfec99c04b6bc8777a">SketchElement::DirectionOfRepresentation</a> &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a5824f352fd89f69c9acc14430a3aa6cd">directions_of_reads</a> () const =0</td></tr>
<tr class="memdesc:a5824f352fd89f69c9acc14430a3aa6cd"><td class="mdescLeft">&#160;</td><td class="mdescRight">returns an array of directions in which sketch elements were read  <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a5824f352fd89f69c9acc14430a3aa6cd">More...</a><br /></td></tr>
<tr class="separator:a5824f352fd89f69c9acc14430a3aa6cd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac59d309eeb226592a96622fec2b307fd"><td class="memItemLeft" align="right" valign="top">virtual const std::string &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac59d309eeb226592a96622fec2b307fd">read_id_to_read_name</a> (const read_id_t read_id) const =0</td></tr>
<tr class="memdesc:ac59d309eeb226592a96622fec2b307fd"><td class="mdescLeft">&#160;</td><td class="mdescRight">returns read name of read with the given read_id  <a href="classclaragenomics_1_1cudamapper_1_1Index.html#ac59d309eeb226592a96622fec2b307fd">More...</a><br /></td></tr>
<tr class="separator:ac59d309eeb226592a96622fec2b307fd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af44999c8852d5915d585c55a1a95c74a"><td class="memItemLeft" align="right" valign="top">virtual const thrust::device_vector&lt; representation_t &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a">unique_representations</a> () const =0</td></tr>
<tr class="memdesc:af44999c8852d5915d585c55a1a95c74a"><td class="mdescLeft">&#160;</td><td class="mdescRight">returns an array where each representation is recorder only once, sorted by representation  <a href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a">More...</a><br /></td></tr>
<tr class="separator:af44999c8852d5915d585c55a1a95c74a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af4f69a9003fedb9ca11665d5faa43bff"><td class="memItemLeft" align="right" valign="top">virtual const thrust::device_vector&lt; std::uint32_t &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af4f69a9003fedb9ca11665d5faa43bff">first_occurrence_of_representations</a> () const =0</td></tr>
<tr class="memdesc:af4f69a9003fedb9ca11665d5faa43bff"><td class="mdescLeft">&#160;</td><td class="mdescRight">returns first occurrence of corresponding representation from <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a" title="returns an array where each representation is recorder only once, sorted by representation">unique_representations()</a> in data arrays  <a href="classclaragenomics_1_1cudamapper_1_1Index.html#af4f69a9003fedb9ca11665d5faa43bff">More...</a><br /></td></tr>
<tr class="separator:af4f69a9003fedb9ca11665d5faa43bff"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a59186cdd6dbfd21baeb07e80bd4354d4"><td class="memItemLeft" align="right" valign="top">virtual const std::uint32_t &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a59186cdd6dbfd21baeb07e80bd4354d4">read_id_to_read_length</a> (const read_id_t read_id) const =0</td></tr>
<tr class="memdesc:a59186cdd6dbfd21baeb07e80bd4354d4"><td class="mdescLeft">&#160;</td><td class="mdescRight">returns read length for the read with the gived read_id  <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a59186cdd6dbfd21baeb07e80bd4354d4">More...</a><br /></td></tr>
<tr class="separator:a59186cdd6dbfd21baeb07e80bd4354d4"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac9e936ae3809c82894a22a5ddb6bb937"><td class="memItemLeft" align="right" valign="top">virtual std::uint64_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#ac9e936ae3809c82894a22a5ddb6bb937">number_of_reads</a> () const =0</td></tr>
<tr class="memdesc:ac9e936ae3809c82894a22a5ddb6bb937"><td class="mdescLeft">&#160;</td><td class="mdescRight">returns number of reads in input data  <a href="classclaragenomics_1_1cudamapper_1_1Index.html#ac9e936ae3809c82894a22a5ddb6bb937">More...</a><br /></td></tr>
<tr class="separator:ac9e936ae3809c82894a22a5ddb6bb937"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr class="memitem:af9247d4b637615bf5912acc57b27b919"><td class="memItemLeft" align="right" valign="top">static uint64_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">maximum_kmer_size</a> ()</td></tr>
<tr class="memdesc:af9247d4b637615bf5912acc57b27b919"><td class="mdescLeft">&#160;</td><td class="mdescRight">Return the maximum kmer length allowable.  <a href="classclaragenomics_1_1cudamapper_1_1Index.html#af9247d4b637615bf5912acc57b27b919">More...</a><br /></td></tr>
<tr class="separator:af9247d4b637615bf5912acc57b27b919"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a47c3cb89daa4076243dd5977acfb7ccf"><td class="memItemLeft" align="right" valign="top">static std::unique_ptr&lt; <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#a47c3cb89daa4076243dd5977acfb7ccf">create_index</a> (const <a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html">io::FastaParser</a> &amp;parser, const read_id_t first_read_id, const read_id_t past_the_last_read_id, const std::uint64_t kmer_size, const std::uint64_t window_size, const bool hash_representations=true)</td></tr>
<tr class="memdesc:a47c3cb89daa4076243dd5977acfb7ccf"><td class="mdescLeft">&#160;</td><td class="mdescRight">generates a mapping of (k,w)-kmer-representation to all of its occurrences for one or more sequences  <a href="classclaragenomics_1_1cudamapper_1_1Index.html#a47c3cb89daa4076243dd5977acfb7ccf">More...</a><br /></td></tr>
<tr class="separator:a47c3cb89daa4076243dd5977acfb7ccf"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a> - manages mapping of (k,w)-kmer-representation and all its occurences. </p>
</div><h2 class="groupheader">Member Function Documentation</h2>
<a id="a47c3cb89daa4076243dd5977acfb7ccf"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a47c3cb89daa4076243dd5977acfb7ccf">&#9670;&nbsp;</a></span>create_index()</h2>

<div class="memitem">
<div class="memproto">
<table class="mlabels">
  <tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
          <td class="memname">static std::unique_ptr&lt;<a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a>&gt; claragenomics::cudamapper::Index::create_index </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html">io::FastaParser</a> &amp;&#160;</td>
          <td class="paramname"><em>parser</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const read_id_t&#160;</td>
          <td class="paramname"><em>first_read_id</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const read_id_t&#160;</td>
          <td class="paramname"><em>past_the_last_read_id</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const std::uint64_t&#160;</td>
          <td class="paramname"><em>kmer_size</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const std::uint64_t&#160;</td>
          <td class="paramname"><em>window_size</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const bool&#160;</td>
          <td class="paramname"><em>hash_representations</em> = <code>true</code>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
        </tr>
      </table>
  </td>
  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">static</span></span>  </td>
  </tr>
</table>
</div><div class="memdoc">

<p>generates a mapping of (k,w)-kmer-representation to all of its occurrences for one or more sequences </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">parser</td><td>parser for the whole input file (part that goes into this index is determined by first_read_id and past_the_last_read_id) </td></tr>
    <tr><td class="paramname">first_read_id</td><td>read_id of the first read to the included in this index </td></tr>
    <tr><td class="paramname">past_the_last_read_id</td><td>read_id+1 of the last read to be included in this index </td></tr>
    <tr><td class="paramname">kmer_size</td><td>k - the kmer length </td></tr>
    <tr><td class="paramname">window_size</td><td>w - the length of the sliding window used to find sketch elements (i.e. the number of adjacent kmers in a window, adjacent = shifted by one basepair) </td></tr>
    <tr><td class="paramname">hash_representations</td><td>- if true, hash kmer representations </td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>instance of <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a> </dd></dl>

</div>
</div>
<a id="a5824f352fd89f69c9acc14430a3aa6cd"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a5824f352fd89f69c9acc14430a3aa6cd">&#9670;&nbsp;</a></span>directions_of_reads()</h2>

<div class="memitem">
<div class="memproto">
<table class="mlabels">
  <tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
          <td class="memname">virtual const thrust::device_vector&lt;<a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a83beb5c091c4b0bfec99c04b6bc8777a">SketchElement::DirectionOfRepresentation</a>&gt;&amp; claragenomics::cudamapper::Index::directions_of_reads </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
  </td>
  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">pure virtual</span></span>  </td>
  </tr>
</table>
</div><div class="memdoc">

<p>returns an array of directions in which sketch elements were read </p>
<dl class="section return"><dt>Returns</dt><dd>an array of directions in which sketch elements were read </dd></dl>

</div>
</div>
<a id="af4f69a9003fedb9ca11665d5faa43bff"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af4f69a9003fedb9ca11665d5faa43bff">&#9670;&nbsp;</a></span>first_occurrence_of_representations()</h2>

<div class="memitem">
<div class="memproto">
<table class="mlabels">
  <tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
          <td class="memname">virtual const thrust::device_vector&lt;std::uint32_t&gt;&amp; claragenomics::cudamapper::Index::first_occurrence_of_representations </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
  </td>
  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">pure virtual</span></span>  </td>
  </tr>
</table>
</div><div class="memdoc">

<p>returns first occurrence of corresponding representation from <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a" title="returns an array where each representation is recorder only once, sorted by representation">unique_representations()</a> in data arrays </p>
<dl class="section return"><dt>Returns</dt><dd>first occurrence of corresponding representation from <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html#af44999c8852d5915d585c55a1a95c74a" title="returns an array where each representation is recorder only once, sorted by representation">unique_representations()</a> in data arrays </dd></dl>

</div>
</div>
<a id="af9247d4b637615bf5912acc57b27b919"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af9247d4b637615bf5912acc57b27b919">&#9670;&nbsp;</a></span>maximum_kmer_size()</h2>

<div class="memitem">
<div class="memproto">
<table class="mlabels">
  <tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
          <td class="memname">static uint64_t claragenomics::cudamapper::Index::maximum_kmer_size </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td></td>
        </tr>
      </table>
  </td>
  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">static</span></span>  </td>
  </tr>
</table>
</div><div class="memdoc">

<p>Return the maximum kmer length allowable. </p>
<dl class="section return"><dt>Returns</dt><dd>Return the maximum kmer length allowable </dd></dl>

</div>
</div>
<a id="ac9e936ae3809c82894a22a5ddb6bb937"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ac9e936ae3809c82894a22a5ddb6bb937">&#9670;&nbsp;</a></span>number_of_reads()</h2>

<div class="memitem">
<div class="memproto">
<table class="mlabels">
  <tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
          <td class="memname">virtual std::uint64_t claragenomics::cudamapper::Index::number_of_reads </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
  </td>
  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">pure virtual</span></span>  </td>
  </tr>
</table>
</div><div class="memdoc">

<p>returns number of reads in input data </p>
<dl class="section return"><dt>Returns</dt><dd>number of reads in input data </dd></dl>

</div>
</div>
<a id="a66e5d024befc410221610f454eff7183"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a66e5d024befc410221610f454eff7183">&#9670;&nbsp;</a></span>positions_in_reads()</h2>

<div class="memitem">
<div class="memproto">
<table class="mlabels">
  <tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
          <td class="memname">virtual const thrust::device_vector&lt;position_in_read_t&gt;&amp; claragenomics::cudamapper::Index::positions_in_reads </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
  </td>
  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">pure virtual</span></span>  </td>
  </tr>
</table>
</div><div class="memdoc">

<p>returns an array of starting positions of sketch elements in their reads </p>
<dl class="section return"><dt>Returns</dt><dd>an array of starting positions of sketch elements in their reads </dd></dl>

</div>
</div>
<a id="a59186cdd6dbfd21baeb07e80bd4354d4"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a59186cdd6dbfd21baeb07e80bd4354d4">&#9670;&nbsp;</a></span>read_id_to_read_length()</h2>

<div class="memitem">
<div class="memproto">
<table class="mlabels">
  <tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
          <td class="memname">virtual const std::uint32_t&amp; claragenomics::cudamapper::Index::read_id_to_read_length </td>
          <td>(</td>
          <td class="paramtype">const read_id_t&#160;</td>
          <td class="paramname"><em>read_id</em></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
  </td>
  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">pure virtual</span></span>  </td>
  </tr>
</table>
</div><div class="memdoc">

<p>returns read length for the read with the gived read_id </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">read_id</td><td></td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>read length for the read with the gived read_id </dd></dl>

</div>
</div>
<a id="ac59d309eeb226592a96622fec2b307fd"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ac59d309eeb226592a96622fec2b307fd">&#9670;&nbsp;</a></span>read_id_to_read_name()</h2>

<div class="memitem">
<div class="memproto">
<table class="mlabels">
  <tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
          <td class="memname">virtual const std::string&amp; claragenomics::cudamapper::Index::read_id_to_read_name </td>
          <td>(</td>
          <td class="paramtype">const read_id_t&#160;</td>
          <td class="paramname"><em>read_id</em></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
  </td>
  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">pure virtual</span></span>  </td>
  </tr>
</table>
</div><div class="memdoc">

<p>returns read name of read with the given read_id </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">read_id</td><td></td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>read name of read with the given read_id </dd></dl>

</div>
</div>
<a id="a5cfe03b47850170ec64d61d2dbef0401"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a5cfe03b47850170ec64d61d2dbef0401">&#9670;&nbsp;</a></span>read_ids()</h2>

<div class="memitem">
<div class="memproto">
<table class="mlabels">
  <tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
          <td class="memname">virtual const thrust::device_vector&lt;read_id_t&gt;&amp; claragenomics::cudamapper::Index::read_ids </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
  </td>
  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">pure virtual</span></span>  </td>
  </tr>
</table>
</div><div class="memdoc">

<p>returns an array of reads ids for sketch elements </p>
<dl class="section return"><dt>Returns</dt><dd>an array of reads ids for sketch elements </dd></dl>

</div>
</div>
<a id="a876d5e82f9fc36f481854f7d84e5fc80"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a876d5e82f9fc36f481854f7d84e5fc80">&#9670;&nbsp;</a></span>representations()</h2>

<div class="memitem">
<div class="memproto">
<table class="mlabels">
  <tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
          <td class="memname">virtual const thrust::device_vector&lt;representation_t&gt;&amp; claragenomics::cudamapper::Index::representations </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
  </td>
  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">pure virtual</span></span>  </td>
  </tr>
</table>
</div><div class="memdoc">

<p>returns an array of representations of sketch elements </p>
<dl class="section return"><dt>Returns</dt><dd>an array of representations of sketch elements </dd></dl>

</div>
</div>
<a id="af44999c8852d5915d585c55a1a95c74a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af44999c8852d5915d585c55a1a95c74a">&#9670;&nbsp;</a></span>unique_representations()</h2>

<div class="memitem">
<div class="memproto">
<table class="mlabels">
  <tr>
  <td class="mlabels-left">
      <table class="memname">
        <tr>
          <td class="memname">virtual const thrust::device_vector&lt;representation_t&gt;&amp; claragenomics::cudamapper::Index::unique_representations </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
  </td>
  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">pure virtual</span></span>  </td>
  </tr>
</table>
</div><div class="memdoc">

<p>returns an array where each representation is recorder only once, sorted by representation </p>
<dl class="section return"><dt>Returns</dt><dd>an array where each representation is recorder only once, sorted by representation </dd></dl>

</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>cudamapper/include/claragenomics/cudamapper/<a class="el" href="index_8hpp_source.html">index.hpp</a></li>
</ul>
</div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by &#160;<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.16
</small></address>
</body>
</html>
